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9 results for “Isolation-by-distance”
Isolation-by-distance and genetic parentage analysis provide similar larval dispersal estimates
<p>An R studio project that includes original SNP data files used to quantify dispersal in <em>Elacatinus lori</em> via the isolation-by-distance (IBD) method. Associated R-code used to generate IBD regression slopes, calculate sigma, and construct dispersal kernels. Includes output from NeEstimator, estimating effective population size. </p> <p>Folders 1-3 contain the code/data needed to obtain the slope of the IBD relationship, effective population size, and the standard deviation (sigma) of the dispersal distribution, respectively. Folder 4 contains the R code needed to construct Laplacian dispersal kernels. </p>
Data from: Genomic data clarify Aquarana systematics and reveal isolation-by-distance dominates phylogeography of the wide-ranging frog Rana clamitans
<p>Wide-ranging species are often polytypic, span geographic dispersal barriers, and experience opportunities for divergence via genetic drift or natural selection. Such conditions can be favorable for speciation and wide-ranging taxa are frequently subdivided into multiple species by modern molecular studies. However, with wide-ranging species, it is important to explicitly test for isolation-by-distance (IBD) which can produce continuous genetic variation that may be misinterpreted as discrete population structure or even distinct species. Here we examine the Green Frog (<em>Rana clamitans</em>), a wide-ranging species of the Aquarana<em> </em>clade distributed across much of North America. Although <em>Rana clamitans</em> is phenotypically variable enough to previously merit description of two subspecies, patterns of genetic diversity remain unclear. Additionally, the broader phylogenetic context for <em>R. clamitans</em> is poorly understood, particularly its relationship with the closely related and IUCN Vulnerable Bog Frog (<em>Rana okaloosae</em>). Using genome-wide ddRAD markers, we largely resolve relationships within Aquarana<em> </em>and unambiguously identify <em>R. okaloosae </em>as the sister lineage to <em>R. clamitans</em>. Within <em>R. clamitans </em>we find two well-supported and geographically divided clades which are identified as distinct species by a widely used genetic species delimitation method, BPP. However, the two clades exhibit low genealogical divergence and population genetic analyses reveal that genetic variation within <em>R. clamitans</em> is best described by a pattern of IBD rather than independently evolving lineages. We conclude that <em>R. clamitans </em>is<em> </em>indeed a single species and the subspecies concept is of limited use. Our analysis emphasizes how existing approaches can erroneously split species characterized by continuous genetic variation and highlights the power of combining population genetic and phylogenetic perspectives to better understand diversity within wide-ranging taxa.</p>
Data from: Genomic data clarify Aquarana systematics and reveal isolation-by-distance dominates phylogeography of the wide-ranging frog Rana clamitans
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Pleistocene speciation and isolation-by-distance within North American mud and rainbow snakes
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Using isolation-by-distance to jointly estimate effective population density and dispersal distance: a practical evaluation using bumble bees
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Data from: Jointly representing long-range genetic similarity and spatially heterogeneous isolation-by-distance
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Data from: Population assignment and local adaptation along an isolation-by-distance gradient in Pacific cod (Gadus macrocephalus)
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Data from: Isolation-by-distance in landscapes: considerations for landscape genetics
In landscape genetics, isolation-by-distance (IBD) is regarded as a baseline pattern that is obtained without additional effects of landscape elements on gene flow. However, the configuration of suitable habitat patches determines deme topology, which in turn should affect rates of gene flow. IBD patterns can be characterized either by monotonically increasing pairwise genetic differentiation (for example, FST) with increasing interdeme geographic distance (case-I pattern) or by monotonically increasing pairwise genetic differentiation up to a certain geographical distance beyond which no correlation is detectable anymore (case-IV pattern). We investigated if landscape configuration influenced the rate at which a case-IV pattern changed to a case-I pattern. We also determined at what interdeme distance the highest correlation was measured between genetic differentiation and geographic distance and whether this distance corresponded to the maximum migration distance. We set up a population genetic simulation study and assessed the development of IBD patterns for several habitat configurations and maximum migration distances. We show that the rate and likelihood of the transition of case-IV to case-I FST–distance relationships was strongly influenced by habitat configuration and maximum migration distance. We also found that the maximum correlation between genetic differentiation and geographic distance was not related to the maximum migration distance and was measured across all deme pairs in a case-I pattern and, for a case-IV pattern, at the distance where the FST–distance curve flattens out. We argue that in landscape genetics, separate analyses should be performed to either assess IBD or the landscape effects on gene flow.
Data from: Isolation-by-distance in landscapes: considerations for landscape genetics
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.